Yes, this looks like an imaging problem--if you have iwrap = 1 in your
&cntrl, the homoDIMERIC protein is two molecules, so each will be re-imaged
separately. The same mechanics that are likely creating your spike are
also the reason that iwrap = 1 can cause simulations with positional
restraints to break unexpectedly hundreds of ns into an otherwise stable
trajectory. (Just posting to bring up that second point, which periodically
pops up on the list, no pun intended.)
Dave
On Tue, Sep 8, 2020 at 11:59 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Did you visualize the trajectory? That will tell you if it is an imaging
> problem or not ( most likely it is)
>
>
> On Tue, Sep 8, 2020 at 11:43 AM Jorge da Rocha <jdarocha1.gmail.com>
> wrote:
>
> > Dear Amber Users,
> >
> > I am running a simulation of a large homodimeric protein (15800 atoms).
> The
> > simulation mostly runs well, but a large tower/spike of RMSD around
> 240ns.
> >
> > I have tried to address the artefact by using autoimage, and anchoring to
> > the residues of the structure, but the issue persists.
> >
> > I am using pmemd.cuda for the simulation.
> >
> > Have you any advice of how to resolve this, or ideas of what could be
> > causing this? I will be rerunning that section of simulation in the mean
> > time to see if anything changes.
> >
> > Warm Regards
> > Jorge da Rocha
> > --
> > Jorge da Rocha (MSc Med)
> > PhD Candidate at the Sydney Brenner Institute for Molecular Bioscience
> > Division of Human Genetics, Faculty of Health Sciences
> > University of the Witwatersrand
> > Cell: 082 944 1651
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Sep 08 2020 - 09:30:02 PDT
